Contacts of the helix formed by residues 92 - 109 (chain E) in PDB entry 1WOH
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 92 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93B PRO* 5.6 2.4 - - - +
154B ASP 3.3 27.2 - - - +
155B THR* 3.1 20.5 + - - -
156B LYS 4.7 0.5 + - - -
157B TRP* 4.4 11.6 + - - -
89E PRO* 3.9 11.8 - - + +
90E SER 3.4 13.2 - - - +
91E LEU* 1.3 81.0 - - - +
93E PRO* 1.3 73.5 - - - +
94E GLN* 3.2 2.9 - - - -
95E LEU* 3.1 14.9 + - + +
96E ALA 3.0 17.5 + - - -
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Residues in contact with PRO 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 4.3 34.3 - - + -
92B GLU 5.5 2.2 - - - +
93B PRO* 5.1 12.1 - - + -
38E PHE* 4.7 8.7 - - + -
40E ILE* 5.3 0.4 - - + -
91E LEU* 3.1 8.7 - - + +
92E GLU* 1.3 87.8 - - - +
94E GLN* 1.3 59.3 + - + +
96E ALA* 3.2 7.0 + - + +
97E HIS* 2.9 44.5 + - - +
157E TRP* 4.3 21.8 - - + +
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Residues in contact with GLN 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E GLU 3.2 1.2 - - - -
93E PRO* 1.3 82.9 - - + +
95E LEU* 1.3 61.9 + - - +
97E HIS* 3.4 15.5 + - + +
98E ASP* 3.2 30.9 + - - +
157E TRP* 4.6 21.2 + - + +
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Residues in contact with LEU 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ASP* 3.8 24.2 - - + +
89E PRO* 3.8 13.5 - - + -
92E GLU* 3.1 19.7 + - + +
94E GLN* 1.3 74.7 - - - +
96E ALA* 1.3 66.7 + - - +
98E ASP* 3.1 12.8 + - + +
99E ARG* 2.9 63.7 + - + +
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Residues in contact with ALA 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E PHE* 4.0 25.8 - - + -
88E LEU* 4.1 10.8 - - + -
89E PRO* 3.8 23.9 - - + +
91E LEU 4.6 0.7 - - - +
92E GLU 3.0 12.1 + - - +
93E PRO* 3.4 9.0 - - + +
95E LEU* 1.3 77.2 - - - +
97E HIS* 1.3 57.7 + - + +
99E ARG* 3.1 4.9 + - - +
100E ILE* 2.9 38.4 + - + +
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Residues in contact with HIS 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E PHE* 5.0 10.2 - + - -
93E PRO* 2.9 32.8 + - + +
94E GLN* 3.4 13.8 - - + +
95E LEU 3.2 0.2 - - - -
96E ALA* 1.3 79.4 - - + +
98E ASP* 1.3 57.6 + - - +
100E ILE* 3.3 3.6 + - + -
101E THR* 3.0 24.8 + - - -
122E SER* 5.1 7.5 + - - -
125E TYR* 4.2 14.0 - + - -
126E PRO* 3.3 31.2 - - + +
129E ARG* 3.0 23.8 + - - +
157E TRP* 3.6 53.9 + + + +
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Residues in contact with ASP 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94E GLN* 3.2 21.8 + - - +
95E LEU* 3.1 16.0 + - + +
97E HIS* 1.3 73.5 - - - +
99E ARG* 1.3 66.1 + - - +
101E THR* 3.4 1.7 + - - -
102E GLU* 3.0 25.8 + - - +
129E ARG* 3.1 23.2 + - - +
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Residues in contact with ARG 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A PRO* 3.8 27.2 - - - +
154B ASP* 2.7 32.5 + - - -
86E VAL* 3.7 17.7 - - + +
87E ILE* 2.8 35.5 + - - +
88E LEU* 4.0 1.3 - - + -
89E PRO* 3.7 16.8 - - - +
95E LEU* 2.9 43.9 + - + +
96E ALA* 3.1 10.5 + - - +
98E ASP* 1.3 75.9 - - + +
100E ILE* 1.3 63.1 + - - +
102E GLU* 4.0 3.6 - - - +
103E ALA* 3.1 26.0 + - - +
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Residues in contact with ILE 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E VAL* 3.4 34.1 - - + -
38E PHE* 5.1 5.2 - - + -
86E VAL* 4.0 10.9 - - + +
88E LEU* 3.9 17.3 - - + -
96E ALA* 2.9 27.6 + - + +
97E HIS* 3.6 7.6 - - + +
99E ARG* 1.3 73.9 - - - +
101E THR* 1.3 60.0 + - - +
103E ALA* 3.4 1.2 + - - +
104E ALA* 2.9 29.5 + - - +
123E VAL* 4.5 7.2 - - + +
126E PRO* 3.8 28.0 - - + -
127E LEU* 3.5 28.9 - - + +
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Residues in contact with THR 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E HIS 3.0 9.5 + - - -
98E ASP* 3.4 3.6 + - - -
100E ILE* 1.3 74.7 - - - +
102E GLU* 1.3 62.8 + - - +
104E ALA* 3.2 4.3 + - - +
105E ARG* 2.9 51.3 + - - +
126E PRO 2.7 22.5 + - - +
129E ARG* 2.9 51.7 + - + +
130E ALA 4.0 3.8 - - - +
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Residues in contact with GLU 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E ASP 3.0 15.9 + - - +
99E ARG* 4.0 4.0 - - - +
101E THR* 1.3 78.7 - - - +
103E ALA* 1.3 63.6 + - - +
105E ARG* 3.2 18.9 + - - +
106E GLN* 3.0 56.4 + - - +
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Residues in contact with ALA 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E PRO* 4.4 8.2 - - + +
34E LEU* 3.9 10.3 - - + -
86E VAL* 3.7 27.6 - - + -
99E ARG 3.1 18.4 + - - +
100E ILE 3.8 0.4 - - - +
102E GLU* 1.3 77.2 - - - +
104E ALA* 1.3 63.1 + - - +
106E GLN* 3.3 16.2 + - - +
107E VAL* 3.0 28.6 + - - +
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Residues in contact with ALA 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E LEU* 3.8 9.8 - - + +
100E ILE 2.9 19.9 + - - +
101E THR* 3.5 5.6 - - - +
103E ALA* 1.3 78.8 - - - +
105E ARG* 1.3 56.5 + - - +
107E VAL* 3.5 2.0 + - - +
108E ARG* 3.0 31.7 + - - +
116E PHE* 3.9 22.5 - - + -
127E LEU* 4.0 14.1 - - + +
130E ALA* 3.6 17.7 - - + -
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Residues in contact with ARG 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E THR* 2.9 31.5 + - - +
102E GLU* 3.2 23.1 + - - +
104E ALA* 1.3 74.3 - - - +
106E GLN* 1.3 67.2 + - + +
108E ARG* 3.2 7.8 + - - +
109E GLY* 3.0 20.3 + - - -
129E ARG* 3.1 23.8 + - - +
130E ALA* 3.6 26.2 + - + +
132E ALA* 4.5 9.9 - - - +
133E ASP* 6.0 4.2 - - - -
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Residues in contact with GLN 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E PRO* 3.5 26.8 - - - +
24E ASP* 3.5 27.5 - - + +
102E GLU* 3.0 42.0 + - - +
103E ALA* 3.4 21.5 + - - +
105E ARG* 1.3 76.8 - - + +
107E VAL* 1.3 62.8 + - - +
109E GLY* 3.3 7.7 + - - -
110E ARG* 2.9 33.7 + - - +
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Residues in contact with VAL 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E PRO* 4.1 12.1 - - + -
27E TRP* 4.1 9.4 - - + -
32E ALA* 3.7 30.5 - - + +
34E LEU* 4.1 22.2 - - + -
83E ALA* 3.8 25.6 - - + -
103E ALA 3.0 17.2 + - - +
104E ALA* 3.9 5.6 - - - +
106E GLN* 1.3 74.6 - - - +
108E ARG* 1.3 64.8 + - - +
110E ARG* 3.1 13.3 + - - +
111E CYS* 3.4 16.1 + - - +
114E PRO* 4.4 11.4 - - + -
116E PHE* 5.2 1.1 - - + -
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Residues in contact with ARG 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E ALA 3.0 20.9 + - - +
105E ARG* 3.2 7.8 + - - +
107E VAL* 1.3 77.6 - - - +
109E GLY* 1.3 56.7 + - - +
110E ARG 3.1 0.2 - - - -
111E CYS* 3.1 28.5 - - - +
112E ARG 6.0 0.7 - - - -
114E PRO* 3.9 22.0 - - + -
116E PHE* 4.7 1.1 - - + -
130E ALA* 2.9 24.4 + - + +
131E PHE* 3.3 47.4 - - + +
133E ASP* 2.6 35.3 + - - -
134E VAL* 3.7 11.7 - - - +
268E VAL* 4.2 9.2 + - - +
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Residues in contact with GLY 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105E ARG 3.0 14.4 + - - -
106E GLN 3.3 3.3 + - - -
107E VAL 3.2 0.8 - - - -
108E ARG* 1.3 74.7 - - - +
110E ARG* 1.3 68.4 + - - +
111E CYS 3.7 0.7 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il